The Zoombinis are a race of small blue creatures depicted with varying facial features, initially living in prosperous peace on a small island called Zoombini Isle; but later enslaved by their neighbors, the Bloats. The game then depicts the Zoombinis' search for a new home, featuring a variety of logical puzzles which the player must solve.

Most of the puzzles involve the physical features of the Zoombinis as part of the solution. For example, in the puzzle 'Allergic Cliffs', the player is given a choice of 2 bridges, each of which will allow Zoombinis to pass only if they have certain combinations of features. The list of available features is as follows:

Hair: Shaggy hair, a ponytail, flattop hair, small tuft, and bob hair with a cap

In total, there are 625 unique combinations, of which the game allows you to make up to two Zoombinis with each combination, making 1,250 possible Zoombinis in total. Of these, 625 must be saved in order to win the game.

The Zoombinis travel in groups of 16 across a series of puzzles. There are 12 puzzles in total, split into four sections, and the Zoombinis must complete 9 puzzles to establish their new home at 'Zoombiniton' ('Zoombiniville' in US version). The first and last 'legs' are compulsory and are completed by all Zoombinis; for the second leg the player is given a choice to take either the north or the south path. Between each 'leg' is a campsite where the Zoombinis can be stored for later retrieval.

If the player successfully brings an entire party of 16 Zoombinis through a leg, the leg will increase in difficulty and a building will be constructed at Zoombiniton/Zoombiniville to celebrate. The four difficulty levels are 'Not So Easy', 'Oh So Hard', 'Very Hard', and 'Very Very Hard', and each difficulty level is color-coded. Once a leg has increased in difficulty, there is no way to reverse the change. If a group of 16 Zoombinis complete a leg while the difficulty is Very Very Hard, the difficulty does not increase; whereas completing a leg under the Very Very Hard difficulty level will only reward the player with a new building once, since there is only one building per leg at each difficulty level.

Here are two bridges across a crevasse, supported by six wooden pegs. Individual Zoombinis can only cross one of the bridges, and the bridge that any Zoombini is allowed to cross is determined by facial characteristics. If the wrong bridge is selected, the face embedded in the cliff will sneeze and the Zoombini will be sent tumbling back to the initial side, whereupon a peg will fall into the crevice. If all six pegs come loose, the bridges collapse and the Zoombinis who did not cross are unable to do so. If the player moves the same Zoombini to each of the two bridges (where the first bridge was wrong and the second bridge correct), the player is guaranteed five Zoombinis on the other side.

The Zoombinis arrive at a stone face divided into four caves, accessed by one path each. Each path is guarded by two stone guardians, who divide the Zoombinis according to features. If the wrong cave is selected, a guardian will release a rock slide, sending the Zoombini to the bottom. The player has many chances to find the right cave for each Zoombini before a rockfall seals the four paths, leaving behind those who have not entered a cave. The stone guards' names are Onyx, Ignorameous, Ferrous, and Crystal.

The Zoombinis arrive on a dirt road guarded by the trolls Arno, Willa, and Shyler, beside a pizza-making machine permitting different toppings for a pizza (cheese, pepperoni, bell peppers, mushrooms, and olives) and ice cream (whipped cream, chocolate syrup, and a cherry). Here the player must create a pizza with unique toppings for each troll. If none of the trolls accept the pizza, it is thrown into a pit; whereas if one of the trolls likes some of the toppings present on the pizza, it will be thrown onto the rock behind that troll. If a troll receives a pizza with all desired toppings, the troll will stand on its rock and wait for the remaining trolls to be satisfied. If the player is unsuccessful in delivering the correct pizza after 6 tries, a troll has the right to strike the Zoombini delivering the pizza and that Zoombini returns to Zoombini Isle, leaving another to take its place. When all trolls are satisfied, they consume their pizzas and the remaining Zoombinis continue their journey.

There are significant changes to the puzzle as the level of difficulty increases:

Not So Easy: Only Arno is present, and there are five pizza toppings.

Oh, So Hard: Willa is added, and there are now four pizza toppings, and ice cream is added with a total of 2 toppings.

Very Hard: Shyler is added. Ice cream toppings remain the same as the preceding level, but all five pizza toppings can now be used. No toppings are liked by more than one troll, but the three trolls will combine to like all the toppings.

Very, Very Hard: Four pizzas are already in the pit, and there are now three ice cream toppings.

Once this leg is complete, the remaining Zoombinis will arrive at Shelter Rock, the first campsite. The player is then given the opportunity to take either the north or the south path to the next leg if they have 16 Zoombinis present. If the player does not have enough Zoombinis, or if they decide to return to a different campsite, the player can place any remaining Zoombinis into a storage compartment.

Captain Cajun takes the Zoombinis across a river on his ferry boat, but only if each passenger has a feature in common with the adjacent Zoombini. If this does not occur, Captain Cajun will taunt the Zoombini and launch the Zoombini off the boat. If one Zoombini tries to sit on a seat already taken, Captain Cajun will taunt the Zoombini again and the Zoombini returns to the group. As the puzzle difficulty increases, the seats become closer together, so each Zoombini must have something in common with multiple Zoombinis.

On the first level, the Zoombinis are placed in a line where fourteen of them must have something in common with two other Zoombinis and the other two just only needs something common with one other Zoombini. On the second level, the Zoombinis are placed on a 2 by 8 grid. On the third level, the Zoombinis are placed on a 4 by 4 grid. The final level is a 4 by 4 grid with the rows shifted slightly. Here, some spaces require one Zoombini to share something in common with six other Zoombinis, as opposed to four.

The player must find a path among a grid of different-shaped, patterned, and colored lily pads, across which the Zoombinis are carried by the eponymous toads, whereof the markings of each correspond to a particular feature distinguishing the path. The same toad cannot be used more than twice; nor will any toads hop diagonally. If the player chooses a path which does not continue across the grid, the toad and Zoombini remain in the grid.

When the puzzle's difficulty increases, a fairy is shown at the beginning of the puzzle changing the lily pads with a wand. The wand (called the "Swapping Stick") is left with the toads and the player must use it assembling a path, until the wand's use is exhausted. In the third and fourth levels, crabs obstruct the toads' pathway, or even misdirect them.

Similar to Captain Cajun's Ferryboat, in that the Zoombinis must be arranged on stones so that each Zoombini has one particular feature in common with its neighbor on the next stone, identified by a small etching on the stone between them. Doing so will create an electric charge (indicated by the stones turning red or blue). Upon completion of this arrangement, the Zoombinis continue. In 'Very Very Hard' Mode (Red, Level 4) of this activity, in the centre of the field usually will be a line of four stones (starting with the main stone furthest right and the other three directly left of it). Linking Zoombinis on these four stones, and these four stones only, a banner stating that the player has entered the 'Psychedelic ZB Zone' where the Zoombinis will start to flash, for visual effect only.

The Zoombinis meet their estranged cousins, the Fleens, in a clearing. There are three Fleens on a tree branch, which must be lured from it by a Zoombini who has characteristics that correspond to the Fleen's characteristics. The object of this puzzle is to deduce which Zoombini characteristics correspond to the Fleen characteristics. When a Fleen is lured off the branch by a Zoombini, it chases the Zoombini until the Zoombini escapes onto another tree branch. The player has six attempts to match the Zoombini with the Fleen before individual Zoombinis fall from the tree, to be chased away by their Fleen equivalents. If all three Fleens on the tree branch are lured off, the remaining Fleens are chased away by bees in formation of a pair of scissors, an arrow, or a storm cloud.

If the 16th and last Zoombini lures the last Fleen off the branch, the player is guaranteed six Zoombinis in the next challenge.

Upon welcome to Didimension Hotel, the player must arrange the Zoombinis in the Hotel's compartments, again divided by characteristics. If a Zoombini is placed in the wrong compartment, the ledge holding the Zoombini will retract and the Zoombini will fall, whereupon the adjacent clock causes 5 minutes to pass. If the clock reaches midnight, all the ledges will retract, and the Zoombinis remaining must return to the previous base camp. As the difficulty increases, more rooms are added, or made inaccessible by Fleens, and the clock disappears. The first level has 5 rooms, the second has 25 rooms, the third has 25 rooms with some rooms boarded up, and the fourth level has 125 rooms and no clock.

Puzzle type - Trial and error, Pattern finding. A large stone wall blocks the path of the Zoombinis; but a nearby machine creates mud balls colored and stamped with a geometric shape. If the mud balls hit a certain target on the wall, either one, two or three Zoombinis are launched over the wall to safety. Eventually, the mud in the machine will run out, stranding the remaining Zoombinis. As the difficulty increases, additional squares require the player to pick the correct shape, mud colour, and colour inside the shape, and the color pattern will shift diagonally.

The Zoombinis encounter a cave where a large stone lion guards the only way onward, and to which the Zoombinis are permitted by a portcullis supported by pegs. Below the lion is a path of 16 stones. The Zoombinis must be placed on the path, in order, according to certain characteristics shown on the wall. If a Zoombini is placed on the wrong stone, that Zoombini is transported to the correct stone and a peg is released. When all the pegs are gone, the portcullis falls and the Zoombinis behind it cannot continue. If a Zoombini is accidentally dropped in the adjacent abyss, that Zoombini is thrown back out, but no peg is lost. The Zoombinis placed correctly on the path are allowed by the lion to continue their journey. As the difficulty increases, characteristics disappear from the wall until none are shown.

The player is presented with a set of glass slides, each bearing the image of a Zoombini, which must be chosen to match a slide featuring its doppelganger, facing it across a large, crystal pendulum. If this is done correctly, the pendulum is lifted and the Zoombini, riding a mine cart, will jump across a shaft and proceed. If it is done incorrectly, the pendulum is lowered and the Zoombini will crash into it and fall down the shaft.

As difficulty increases, the original reflections are modified by additional slides bearing isolate features. Later, the player will be forced to use a particular Zoombini (based on the order in which they left the last challenge), and later still, must use the same set of intervening slides to match the images of two Zoombinis in succession.

The Zoombinis navigate a maze while encased in an air-borne bubble, being transmitted through one of two starting points; and the player has no control over the bubble once it is in motion. Panels at junctions change the direction of some Zoombinis, according to certain characteristics; wherefore an incorrect placement at the start may cause the Zoombini to vanish. If placed correctly, the Zoombinis pass to the other side of the maze. All lost Zoombinis return to the Shade Tree base camp.

As the puzzle's difficulty increases, the Zoombinis can only navigate the maze from one starting point. The player must notice arrows that alternate the directions in which they send Zoombinis, as well as panels that change direction when a bubble passes over a corresponding trigger. Still other panels lock bubbles in place until another bubble passes a release trigger, allowing the trapped bubble to continue. So as not to lose Zoombinis, players must send Zoombinis into the maze in the correct sequence and timing. If two bubbles collide, both Zoombinis will be lost, unless one is locked in place.

Zoombinis who survive this leg reach Zoombiniton. The more Zoombinis complete the journey, the more buildings are built and the bigger the town grows.

The original version of the game by Broderbund Europe in March 1996 came in three languages: British (v1.0BR), French (v1.0FR), and German (v1.0DE). The US division of Broderbund made some minor changes and released a US version (v1.1) in December 1996. As part of the US release they changed the names of several areas of the game as follows:

Zoombiniton was renamed Zoombiniville.

The Marshy Trail was renamed 'Who's Bayou'.

Didimension Hotel was renamed 'Hotel Dimensia'.

In addition the following changes were made to v1.1:

A 32-bit version of the game was added, providing performance improvements for 32-bit operating systems. The 16-bit version remained available for compatibility with Windows 3.x.

A new help feature was added, providing assistance to players who are stuck.

Minor changes were made to some areas. For example, color-changing mushrooms were added to Shelter Rock.

A link to 'Practice Mode' was added to the map screen (previously the player was required to press the keyboard shortcut CTRL+P in order to use Practice Mode)

The rate of advancement through difficulty levels was slowed, meaning that players advance in levels after three successful passes through a leg of puzzles.

The 'save game' format was changed slightly. Saves from v1.0 are compatible with v1.1, but not the other way around.

In February 2015, TERC, the original creator of Zoombinis launched a Kickstarter Campaign to release an updated version of the game for modern tablets and computers. On the 25th of March 2015, the crowdfunding campaign was funded successfully, with the total pledged double the original target of $50,000[1] This updated version is scheduled to be released in Summer 2015.

Rob Pegoraro wrote, "Something that purports to teach "statistical thinking" and "multidimensional arrangements" could be frighteningly dull, but Logical Journey of the Zoombinis, a charming little interactive fairy tale, avoids that fate. ... [The] puzzles require the player to use deductive logic and pattern-matching skills [and while] "Zoombinis" won't teach a child any thing in particular, it will teach a fair amount about how to think about things."[2] Karney praised the game and noted that "...the audio cues make it possible for children with little reading ability to play. Logical Journey of the Zoombinis, a valuable learning aid, actually makes tough mathematical concepts a lot of fun to learn."[3] An article in The Washington Post contained a positive review from a child as part of a follow up to another positive review published two months prior by Don Oldenburg.[4] In 1997, the Logical Journey of the Zoombinis would go on to win in the 12th Annual Excellence in Software Awards, also known as the Codie Awards, in the "Best Home Education for Pre-Teens" category.[5]